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rebuild config

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This commit is contained in:
Laila Los
2022-12-22 16:59:27 +01:00
parent 0ef21dc25a
commit 7d7ac4111b
2 changed files with 16 additions and 160 deletions
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doc/source/admin/galaxy_options.rst
+5 -5
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@@ -5062,15 +5062,15 @@
:Type: bool
~~~~~~~~~~~~~~~
``themes_file``
~~~~~~~~~~~~~~~
~~~~~~~~~~~~~~~~~~~~~~
``themes_config_file``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
Optional file containing one or more themes for galaxy. If several
themes are defined, users can choose their preferd theme in the
themes are defined, users can choose their preferred theme in the
client.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``themes.yml``
:Default: ``themes_conf.yml``
:Type: str
lib/galaxy/config/sample/galaxy.yml.sample
+11 -155
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@@ -20,55 +20,16 @@
# ``uwsgi:`` section will be ignored if Galaxy is started via Gravity commands (e.g ``./run.sh``, ``galaxy`` or ``galaxyctl``).
gravity:
# Process manager to use.
# ``supervisor`` is the default process manager when Gravity is invoked as a non-root user.
# ``systemd`` is the default when Gravity is invoked as root.
# Valid options are: supervisor, systemd
# process_manager:
# What command to write to the process manager configs
# `gravity` (`galaxyctl exec <service-name>`) is the default
# `direct` (each service's actual command) is also supported.
# Valid options are: gravity, direct
# service_command_style: gravity
# Use the process manager's *service instance* functionality for services that can run multiple instances.
# Presently this includes services like gunicorn and Galaxy dynamic job handlers. Service instances are only supported if
# ``service_command_style`` is ``gravity``, and so this option is automatically set to ``false`` if
# ``service_command_style`` is set to ``direct``.
# use_service_instances: true
# umask under which services should be executed. Setting ``umask`` on an individual service overrides this value.
# umask: '022'
# Memory limit (in GB), processes exceeding the limit will be killed. Default is no limit. If set, this is default value
# for all services. Setting ``memory_limit`` on an individual service overrides this value. Ignored if ``process_manager``
# is ``supervisor``.
# memory_limit:
# Specify Galaxy config file (galaxy.yml), if the Gravity config is separate from the Galaxy config. Assumed to be the
# same file as the Gravity config if a ``galaxy`` key exists at the root level, otherwise, this option is required.
# galaxy_config_file:
# Specify Galaxy's root directory.
# Gravity will attempt to find the root directory, but you can set the directory explicitly with this option.
# galaxy_root:
# User to run Galaxy as, required when using the systemd process manager as root.
# Ignored if ``process_manager`` is ``supervisor`` or user-mode (non-root) ``systemd``.
# galaxy_user:
# Group to run Galaxy as, optional when using the systemd process manager as root.
# Ignored if ``process_manager`` is ``supervisor`` or user-mode (non-root) ``systemd``.
# galaxy_group:
# Set to a directory that should contain log files for the processes controlled by Gravity.
# If not specified defaults to ``<galaxy_data_dir>/gravity/log``.
# If not specified defaults to ``<state_dir>/log``.
# log_dir:
# Set to Galaxy's virtualenv directory.
# If not specified, Gravity assumes all processes are on PATH. This option is required in most circumstances when using
# the ``systemd`` process manager.
# If not specified, Gravity assumes all processes are on PATH.
# virtualenv:
# Select the application server.
@@ -82,7 +43,7 @@ gravity:
# this is hidden from you when running a single instance.
# instance_name: _default_
# Configuration for Gunicorn. Can be a list to run multiple gunicorns for rolling restarts.
# Configuration for Gunicorn.
gunicorn:
# Enable Galaxy gunicorn server.
@@ -109,23 +70,6 @@ gravity:
# Consumes less memory when multiple processes are configured. Default is ``false`` if using unicornherder, else ``true``.
# preload:
# umask under which service should be executed
# umask:
# Value of supervisor startsecs, systemd TimeoutStartSec
# start_timeout: 15
# Value of supervisor stopwaitsecs, systemd TimeoutStopSec
# stop_timeout: 65
# Amount of time to wait for a server to become alive when performing rolling restarts.
# restart_timeout: 300
# Memory limit (in GB). If the service exceeds the limit, it will be killed. Default is no limit or the value of the
# ``memory_limit`` setting at the top level of the Gravity configuration, if set. Ignored if ``process_manager`` is
# ``supervisor``.
# memory_limit:
# Extra environment variables and their values to set when running the service. A dictionary where keys are the variable
# names.
# environment: {}
@@ -156,20 +100,6 @@ gravity:
# Extra arguments to pass to Celery command line.
# extra_args:
# umask under which service should be executed
# umask:
# Value of supervisor startsecs, systemd TimeoutStartSec
# start_timeout: 10
# Value of supervisor stopwaitsecs, systemd TimeoutStopSec
# stop_timeout: 10
# Memory limit (in GB). If the service exceeds the limit, it will be killed. Default is no limit or the value of the
# ``memory_limit`` setting at the top level of the Gravity configuration, if set. Ignored if ``process_manager`` is
# ``supervisor``.
# memory_limit:
# Extra environment variables and their values to set when running the service. A dictionary where keys are the variable
# names.
# environment: {}
@@ -187,8 +117,7 @@ gravity:
# port: 4002
# Routes file to monitor.
# Should be set to the same path as ``interactivetools_map`` in the ``galaxy:`` section. This is ignored if
# ``interactivetools_map is set``.
# Should be set to the same path as ``interactivetools_map`` in the ``galaxy:`` section.
# sessions: database/interactivetools_map.sqlite
# Include verbose messages in gx-it-proxy
@@ -206,20 +135,6 @@ gravity:
# This is an advanced option that is only needed when proxying to remote interactive tool container that cannot be reached through the local network.
# reverse_proxy: false
# umask under which service should be executed
# umask:
# Value of supervisor startsecs, systemd TimeoutStartSec
# start_timeout: 10
# Value of supervisor stopwaitsecs, systemd TimeoutStopSec
# stop_timeout: 10
# Memory limit (in GB). If the service exceeds the limit, it will be killed. Default is no limit or the value of the
# ``memory_limit`` setting at the top level of the Gravity configuration, if set. Ignored if ``process_manager`` is
# ``supervisor``.
# memory_limit:
# Extra environment variables and their values to set when running the service. A dictionary where keys are the variable
# names.
# environment: {}
@@ -260,72 +175,6 @@ gravity:
# Extra arguments to pass to tusd command line.
# extra_args:
# umask under which service should be executed
# umask:
# Value of supervisor startsecs, systemd TimeoutStartSec
# start_timeout: 10
# Value of supervisor stopwaitsecs, systemd TimeoutStopSec
# stop_timeout: 10
# Memory limit (in GB). If the service exceeds the limit, it will be killed. Default is no limit or the value of the
# ``memory_limit`` setting at the top level of the Gravity configuration, if set. Ignored if ``process_manager`` is
# ``supervisor``.
# memory_limit:
# Extra environment variables and their values to set when running the service. A dictionary where keys are the variable
# names.
# environment: {}
# Configuration for Galaxy Reports.
reports:
# Enable Galaxy Reports server.
# enable: false
# Path to reports.yml, relative to galaxy.yml if not absolute
# config_file: reports.yml
# The socket to bind. A string of the form: ``HOST``, ``HOST:PORT``, ``unix:PATH``, ``fd://FD``. An IP is a valid HOST.
# bind: localhost:9001
# Controls the number of Galaxy Reports application processes Gunicorn will spawn.
# It is not generally necessary to increase this for the low-traffic Reports server.
# workers: 1
# Gunicorn workers silent for more than this many seconds are killed and restarted.
# Value is a positive number or 0. Setting it to 0 has the effect of infinite timeouts by disabling timeouts for all workers entirely.
# timeout: 300
# URL prefix to serve from.
# The corresponding nginx configuration is (replace <url_prefix> and <bind> with the values from these options):
#
# location /<url_prefix>/ {
# proxy_pass http://<bind>/;
# }
#
# If <bind> is a unix socket, you will need a ``:`` after the socket path but before the trailing slash like so:
# proxy_pass http://unix:/run/reports.sock:/;
# url_prefix:
# Extra arguments to pass to Gunicorn command line.
# extra_args:
# umask under which service should be executed
# umask:
# Value of supervisor startsecs, systemd TimeoutStartSec
# start_timeout: 10
# Value of supervisor stopwaitsecs, systemd TimeoutStopSec
# stop_timeout: 10
# Memory limit (in GB). If the service exceeds the limit, it will be killed. Default is no limit or the value of the
# ``memory_limit`` setting at the top level of the Gravity configuration, if set. Ignored if ``process_manager`` is
# ``supervisor``.
# memory_limit:
# Extra environment variables and their values to set when running the service. A dictionary where keys are the variable
# names.
# environment: {}
@@ -2696,3 +2545,10 @@ galaxy:
# Display built-in converters in the tool panel.
#display_builtin_converters: true
# Optional file containing one or more themes for galaxy. If several
# themes are defined, users can choose their preferred theme in the
# client.
# The value of this option will be resolved with respect to
# <config_dir>.
#themes_config_file: themes_conf.yml